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Ubuntu Linux AMI is partnered by Canonical and same is supported as an custom AMI per [2]. Also, the list of Operating systems supported for EKS custom AMIs are per [3].
On checking, could not see KVM based AMI supported as an custom AMI for EKS Workernodes. Furthermore, check an new issue open in the EKS Custom AMI Github repo [4] and EKS Roadmap issues [5]. You could open an issue in container road-map for feature request.
[1] https://github.com/aws-samples/amazon-eks-custom-amis#amazon-eks-sample-custom-amis
[2] https://docs.aws.amazon.com/eks/latest/userguide/eks-partner-amis.html
[3] https://github.com/aws-samples/amazon-eks-custom-amis#supported-operating-systems
[4] https://github.com/aws-samples/amazon-eks-custom-amis/issues
[5] https://github.com/aws/containers-roadmap/issues
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